generateExprSet-method {affy}R Documentation

generate a set of expression values

Description

Generate a set of expression values from the probe pair information. The set of expression is returned as an exprSet object.

Usage

  computeExprSet(x, pmcorrect.method, summary.method, ...)

  generateExprSet.methods

Arguments

x a AffyBatch holding the probe level informations to generate the expression values.
pmcorrect.method the method used to correct PM values (see section 'details').
summary.method the method used to generate the expression value (see section 'details').
... any of the options of the normalization you would like to modify

Details

An extra argument ids= can be passed. It must be a vector of affids. The expression values will only be computed and returned for these affyids.

The different methods available through this mecanism can be accessed by calling the method generateExprSet.methods with an object of call Cel.container as an argument.

In the Affymetrix design, MM probes were included to measure the noise (or background signal). The original algorithm for background correction was to subtract the MM signal to the PM signal. The methods currently inclluded in the package are "bg.correct.subtractmm", "bg.correct.pmonly" and "bg.correct.adjust".

See Also

method generateExprSet of the class AffyBatch
expresso

Examples

 data(affybatch.example)

 ids <- c( "A28102_at","AB000114_at")
  
  eset <- computeExprSet(affybatch.example, pmcorrect.method="pmonly",
summary.method="avgdiff", ids=ids)

[Package affy version 1.8.1 Index]